That's an easy one. I wanted to remove a certain User from a Site Collection, because it seems that the profile didn't get an update.
1) Head over to Site Permissions
2) Choose any group you want, click on it. The address is something like /_layouts/people.aspx?MembershipGroupID=1
3) Change the ID to 0
Now you will see a list of all Users in that particular SC. You can now remove the Users.